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At least 865 records · Page 48Linked to original sources
USGS2022

hical—The HiRISE radiometric calibration software developed within the ISIS3 planetary image processing suite

Introduction This report summarizes the software and algorithms that are used to calibrate images returned by the High Resolution Imaging Science Experiment (HiRISE) camera onboard the Mars Reconnaissance Orbiter (MRO) spacecraft. The instrument design and data processing methods are summarized below, followed by a description of relevant calibration data and details of the calibration procedure. In this document, we describe the software that uses those coefficients and matrices to radiometrically calibrate HiRISE data. This software is included in version 3 of the Integrated Software for Imagers and Spectrometers (ISIS3), which is developed and maintained by the U.S. Geological Survey Astrogeology Science Center in Flagstaff, Ariz., for the international planetary science community via funding from the National Aeronautics and Space Administration. ISIS3 is freely available to the scientific community and can be obtained at http://isis.astrogeology.usgs.gov/index.html . Support for ISIS3 is provided at https://github.com/USGS-Astrogeology/ISIS3 .

Techniques and Methods↗
USGS2002

Chapter A5. Processing of water samples

The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter addresses methods to be used in processing water samples to be analyzed for inorganic and organic chemical substances, including the bottling of composite, pumped, and bailed samples and subsamples; sample filtration; solid-phase extraction for pesticide analyses; sample preservation; and sample handling and shipping. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.'

Techniques of Water-Resources Investigations↗
USGS1984

Computer model of one-dimensional equilibrium controlled sorption processes

A numerical solution to the one-dimensional solute-transport equation with equilibrium-controlled sorption and a first-order irreversible-rate reaction is presented. The computer code is written in FORTRAN language, with a variety of options for input and output for user ease. Sorption reactions include Langmuir, Freundlich, and ion-exchange, with or without equal valance. General equations describing transport and reaction processes are solved by finite-difference methods, with nonlinearities accounted for by iteration. Complete documentation of the code, with examples, is included. (USGS)

Water-Resources Investigations Report↗
USGS1995

Shallow infiltration processes at Yucca Mountain, Nevada: neutron logging data 1984-93

To determine site suitability of Yucca Mountain, Nevada, as a potential high-level radioactive waste repository, a study was devised to characterize net infiltration. This study involves a detailed data set produced from 99 neutron boreholes that consisted of volumetric water-content readings with depth from 1984 through 1993 at Yucca Mountain. Boreholes were drilled with minimal disturbance to the surrounding soil or rock in order to best represent field conditions. Boreholes were located in topographic positions representing infiltration zones identified as ridgetops, sideslopes, terraces, and active channels. Through careful field calibration, neutron moisture logs, collected on a monthly basis and representing most of the areal locations at Yucca Mountain, illustrated that the depth of penetration of seasonal moisture, important for escaping loss to evapotranspiration, was influenced by several factors. It was increased (1) by thin soil cover, especially in locations where thin soil is underlain by fractured bedrock; (2) on ridgetops; and (3) during the winter when evapotranspiration is low and runoff is less frequent. This data set helps to provide a seasonal and areal distribution of changes in volumetric water content with which to assess hydrologic processes contributing to net infiltration.

Nevada↗
USGS1995

Geochemical processes and the effects of natural organic solutes on the solubility of selenium in coal-mine backfill samples from the Powder River basin, Wyoming

Geochemical processes and the effects of natural organic solutes on the solubility of selenium in coal-mine backfill aquifers were investigated. Backfill and ground-water samples were collected at coal mines in the Powder River Basin, Wyoming. Backfill was generally dominated by aluminum (14,400 to 49,000 mg/kg (milligrams per kilogram)), iron (3,330 to 23,200 mg/kg), and potassium (7,950 to 18,000 mg/kg). Backfill saturated-paste selenium concentrations ranged from 1 to 156 mg/kg (microsiemens per kilogram). Ground-water total selenium concentrations ranged from 3 to 125 mg/L. Dissolved organic carbon in all ground-water samples was dominated by hydrophobic and hydrophilic acids (38 to 84 percent). Selenite sorption/desorption experiments were conducted using background solutions of distilled-deionized water, 0.1 molar calcium chloride, and isolated hydrophobic and hydrophilic acids. Selenite sorption was larger when 0.1 molar calcium chloride was used. The addition of hydrophilic acid decreased selenite sorption more than the addition of hydrophobic acids. Geochemical modelling was used to predict the solid phases controlling dissolved selenium concentrations and to evaluate the effects of dissolved organic carbon on selenium solubility. Results suggested that 55 to 90 percent of selenium in backfill precipitation/dissolution extracts was dominated by magnesium selenate ion pairs. Dissolved organic carbon had little effect on selenium speciation. A redox chamber was constructed to control Eh and pH in water and backfill-core sample suspensions. The response of selenite and selenate in water samples to redox conditions did not follow thermodynamic predictions. Reduction of selenate in water samples did not occur at any of the redox levels tested.

Water-Resources Investigations Report↗
USGS2021

Sea star wasting disease pathology in Pisaster ochraceus shows a basal-to-surface process affecting color phenotypes differently

Sea star wasting disease (SSWD) refers to a suite of poorly described non-specific clinical signs including abnormal posture, epidermal ulceration, and limb autotomy (sloughing) causing mortalities of over 20 species of sea stars and subsequent ecological shifts throughout the northeastern Pacific. While SSWD is widely assumed to be infectious, with environmental conditions facilitating disease progression, few data exist on cellular changes associated with the disease. This is unfortunate, because such observations could inform mechanisms of disease pathogenesis and host susceptibility. Here, we replicated SSWD by exposing captive Pisaster ochraceus to a suite of non-infectious organic substances and show that development of gross lesions is a basal-to-surface process involving inflammation (e.g. infiltration of coelomocytes) of ossicles and mutable collagenous tissue, leading to epidermal ulceration. Affected sea stars also manifest increases in a heretofore undocumented coelomocyte type, spindle cells, that might be a useful marker of inflammation in this species. Finally, compared to purple morphs, orange P. ochraceus developed more severe lesions but survived longer. Longer-lived, and presumably more visible, severely-lesioned orange sea stars could have important demographic implications in terms of detectability of lesioned animals in the wild and measures of apparent prevalence of disease.

Diseases of Aquatic Organisms↗
USGS1999

Processes governing phytoplankton blooms in estuaries. II: The role of horizontal transport

The development and distribution of phytoplankton blooms in estuaries are functions of both local conditions (i.e. the production-loss balance for a water column at a particular spatial location) and large-scale horizontal transport. In this study, the second of a 2-paper series, we use a depth-averaged hydrodynamic-biological model to identify transport-related mechanisms impacting phytoplankton biomass accumulation and distribution on a system level. We chose South San Francisco Bay as a model domain, since its combination of a deep channel surrounded by broad shoals is typical of drowned-river estuaries. Five general mechanisms involving interaction of horizontal transport with variability in local conditions are discussed. Residual (on the order of days to weeks) transport mechanisms affecting bloom development and location include residence time/export, import, and the role of deep channel regions as conduits for mass transport. Interactions occurring on tidal time scales, i.e. on the order of hours) include the phasing of lateral oscillatory tidal flow relative to temporal changes in local net phytoplankton growth rates, as well as lateral sloshing of shoal-derived biomass into deep channel regions during ebb and back into shallow regions during flood tide. Based on these results, we conclude that: (1) while local conditions control whether a bloom is possible, the combination of transport and spatial-temporal variability in local conditions determines if and where a bloom will actually occur; (2) tidal-time-scale physical-biological interactions provide important mechanisms for bloom development and evolution. As a result of both subtidal and tidal-time-scale transport processes, peak biomass may not be observed where local conditions are most favorable to phytoplankton production, and inherently unproductive areas may be regions of high biomass accumulation.

Marine Ecology Progress Series↗
USGS2022

Hydrologic controls on peat permafrost and carbon processes: New insights from past and future modeling

Soil carbon (C) in permafrost peatlands is vulnerable to decomposition with thaw under a warming climate. The amount and form of C loss likely depends on the site hydrology following permafrost thaw, but antecedent conditions during peat accumulation are also likely important. We test the role of differing hydrologic conditions on rates of peat accumulation, permafrost formation, and response to warming at an Arctic tundra fen using a process-based model of peatland dynamics in wet and dry landscape settings that persist from peat initiation in the mid-Holocene through future simulations to 2100 CE and 2300 CE. Climate conditions for both the wet and dry landscape settings are driven by the same downscaled TraCE-21ka transient paleoclimate simulations and CCSM4 RCP8.5 climate drivers. The landscape setting controlled the rates of peat accumulation, permafrost formation and the response to climatic warming and permafrost thaw. The dry landscape scenario had high rates of initial peat accumulation (11.7 ± 3.4 mm decade −1 ) and rapid permafrost aggradation but similar total C stocks as the wet landscape scenario. The wet landscape scenario was more resilient to 21st century warming temperatures than the dry landscape scenario and showed 60% smaller C losses and 70% more new net peat C additions by 2100 CE. Differences in the modeled responses indicate the largest effect is related to the landscape setting and basin hydrology due to permafrost controls on decomposition, suggesting an important sensitivity to changing runoff patterns. These subtle hydrological effects will be difficult to capture at circumpolar scales but are important for the carbon balance of permafrost peatlands under future climate warming.

Frontiers in Environmental Science↗
USGS2018

Rhizophagy cycle: An oxidative process in plants for nutrient extraction from symbiotic microbes

In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.

Microorganisms↗
USGS2008

Relationship between remotely-sensed vegetation indices, canopy attributes and plant physiological processes: What vegetation indices can and cannot tell us about the landscape

Vegetation indices (VIs) are among the oldest tools in remote sensing studies. Although many variations exist, most of them ratio the reflection of light in the red and NIR sections of the spectrum to separate the landscape into water, soil, and vegetation. Theoretical analyses and field studies have shown that VIs are near-linearly related to photosynthetically active radiation absorbed by a plant canopy, and therefore to light-dependent physiological processes, such as photosynthesis, occurring in the upper canopy. Practical studies have used time-series VIs to measure primary production and evapotranspiration, but these are limited in accuracy to that of the data used in ground truthing or calibrating the models used. VIs are also used to estimate a wide variety of other canopy attributes that are used in Soil-Vegetation-Atmosphere Transfer (SVAT), Surface Energy Balance (SEB), and Global Climate Models (GCM). These attributes include fractional vegetation cover, leaf area index, roughness lengths for turbulent transfer, emissivity and albedo. However, VIs often exhibit only moderate, non-linear relationships to these canopy attributes, compromising the accuracy of the models. We use case studies to illustrate the use and misuse of VIs, and argue for using VIs most simply as a measurement of canopy light absorption rather than as a surrogate for detailed features of canopy architecture. Used this way, VIs are compatible with “Big Leaf” SVAT and GCMs that assume that canopy carbon and moisture fluxes have the same relative response to the environment as any single leaf, simplifying the task of modeling complex landscapes.

Arizona↗
USGS2020

Timescale methods for simplifying, understanding and modeling biophysical and water quality processes in coastal aquatic ecosystems: A review

In this article, we describe the use of diagnostic timescales as simple tools for illuminating how aquatic ecosystems work, with a focus on coastal systems such as estuaries, lagoons, tidal rivers, reefs, deltas, gulfs, and continental shelves. Intending this as a tutorial as well as a review, we discuss relevant fundamental concepts (e.g., Lagrangian and Eulerian perspectives and methods, parcels, particles, and tracers), and describe many of the most commonly used diagnostic timescales and definitions. Citing field-based, model-based, and simple algebraic methods, we describe how physical timescales (e.g., residence time, flushing time, age, transit time) and biogeochemical timescales (e.g., for growth, decay, uptake, turnover, or consumption) are estimated and implemented (sometimes together) to illuminate coupled physical-biogeochemical systems. Multiple application examples are then provided to demonstrate how timescales have proven useful in simplifying, understanding, and modeling complex coastal aquatic systems. We discuss timescales from the perspective of “holism”, the degree of process richness incorporated into them, and the value of clarity in defining timescales used and in describing how they were estimated. Our objective is to provide context, new applications and methodological ideas and, for those new to timescale methods, a starting place for implementing them in their own work.

Water↗
USGS2003

Inorganic nitrogen transformations in the bed of the Shingobee River, Minnesota: Integrating hydrologic and biological processes using sediment perfusion cores

Inorganic N transformations were examined in streambed sediments from the Shingobee River using sediment perfusion cores. The experimental design simulated groundwater-stream water mixing within sediment cores, which provided a well-defined one-dimensional representation of in situ hydrologic conditions. Two distinct hydrologic and chemical settings were preserved in the sediment cores: the lowermost sediments, perfused with groundwater, remained anaerobic during the incubations, whereas the uppermost sediments, perfused with oxic water pumped from the overlying water column, simulated stream water penetration into the bed. The maintenance of oxic and anoxic zones formed a biologically active aerobic-anaerobic interface. Ammonium (NH4+) dissolved in groundwater was transported conservatively through the lower core zone but was removed as it mixed with aerated recycle water. Concurrently, a small quantity of nitrate (NO3-) equaling ???25% of the NH4+ loss was produced in the upper sediments. The NH4+ and NO3- profiles in the uppermost sediments resulted from coupled nitrification-denitrification, because assimilation and sorption were negligible. We hypothesize that anaerobic microsites within the aerated upper sediments supported denitrification. Rates of nitrification and denitrification in the perfusion cores ranged 42-209 and 53-160 mg N m-2 day-1, respectively. The use of modified perfusion cores permitted the identification and quantification of N transformations and verified process control by surface water exchange into the shallow hyporheic zone of the Shingobee River.

Minnesota↗
USGS2005

Radium isotopes in Cayuga Lake, New York: Indicators of inflow and mixing processes

Naturally occurring radium isotopes ( 223 Ra, 224 Ra, 226 Ra, and 228 Ra) were measured in lake and tributary water of Cayuga Lake, New York, during the course of a vernal inflow event in the spring of 2001. A large influx of groundwater, probably from a carbonate aquifer, entered the lake at its extreme southern end early in the vernal inflow event and spread northward, covering an extensive part of the southern end of the lake. The low 228 Ra/ 226 Ra activity ratio of this water mass, compared with bulk lake water, allowed its identification through time. Estimates of mixing with bulk lake water were calculated from changes in the 226Ra content. Groundwater inflow to the lake around the delta of a major tributary was detected on the basis of 223 Ra and 224 Ra activity of lake and tributary water. Inflow of a water mass to the surface of the lake was also detected using 223 Ra and 224 Ra activity. The integrity of this water mass was monitored using short‐lived radium isotopes. Suspended sediment in the lake water is a source of the short‐lived radium isotopes 223 Ra (~2 x 10 −4 dpm L −1 ) and 224 Ra (~3 x x 10 −3 dpm L −1 ), but bottom sediments are a more significant source of 228 Ra. Radium isotopes can be valuable new tools in limnological investigations, allowing detection and monitoring of events and processes such as water inflow and mixing, determining sources of inflowing water, and monitoring introduced water masses as they move within the lake.

New York↗
USGS2015

Distribution and biophysical processes of beaded streams in Arctic permafrost landscapes

Beaded streams are widespread in permafrost regions and are considered a common thermokarst landform. However, little is known about their distribution, how and under what conditions they form, and how their intriguing morphology translates to ecosystem functions and habitat. Here we report on a Circum-Arctic survey of beaded streams and a watershed-scale analysis in northern Alaska using remote sensing and field studies. We mapped over 400 channel networks with beaded morphology throughout the continuous permafrost zone of northern Alaska, Canada, and Russia and found the highest abundance associated with medium- to high- ground ice content permafrost in moderately sloping terrain. In the Fish Creek watershed, beaded streams accounted for half of the drainage density, occurring primarily as low-order channels initiating from lakes and drained lake basins. Beaded streams predictably transition to alluvial channels with increasing drainage area and decreasing channel slope, although this transition is modified by local controls on water and sediment delivery. Comparison of one beaded channel using repeat photography between 1948 and 2013 indicate a relatively stable landform and 14C dating of basal sediments suggest channel formation may be as early as the Pleistocene-Holocene transition. Contemporary processes, such as deep snow accumulation in riparian zones effectively insulates channel ice and allows for perennial liquid water below most beaded stream pools. Because of this, mean annual temperatures in pool beds are greater than 2°C, leading to the development of perennial thaw bulbs or taliks underlying these thermokarst features. In the summer, some pools thermally stratify, which reduces permafrost thaw and maintains coldwater habitats. Snowmelt generated peak-flows decrease rapidly by two or more orders of magnitude to summer low flows with slow reach-scale velocity distributions ranging from 0.1 to 0.01 m/s, yet channel runs still move water rapidly between pools. The repeating spatial pattern associated with beaded stream morphology and hydrological dynamics may provide abundant and optimal foraging habitat for fish. Thus, beaded streams may create important ecosystem functions and habitat in many permafrost landscapes and their distribution and dynamics are only beginning to be recognized in Arctic research.

Alaska↗
USGS2023

Steady-state forms of channel profiles shaped by debris flow and fluvial processes

Debris flows regularly traverse bedrock channels that dissect steep landscapes, but our understanding of bedrock erosion by debris flows and their impact on steepland morphology is still rudimentary. Quantitative models of steep bedrock channel networks are based on geomorphic transport laws designed to represent erosion by water-dominated flows. To quantify the impact of debris flow erosion on steep channel network form, it is first necessary to develop methods to estimate spatial variations in bulk debris flow properties (e.g., flow depth, velocity) throughout the channel network that can be integrated into landscape evolution models. Here, we propose and evaluate two methods to estimate spatial variations in bulk debris flow properties along the length of a channel profile. We incorporate both methods into a model designed to simulate the evolution of longitudinal channel profiles that evolve in response to debris flow and fluvial processes. To explore this model framework, we propose a general family of debris flow erosion laws where erosion rate is a function of debris flow depth and channel slope. Model results indicate that erosion by debris flows can explain the occurrence of a scaling break in the slope–area curve at low-drainage areas and that upper-network channel morphology may be useful for inferring catchment-averaged erosion rates in quasi-steady landscapes. Validating specific forms of a debris flow incision law, however, would require more detailed model–data comparisons in specific landscapes where input parameters and channel morphometry can be better constrained. Results improve our ability to interpret topographic signals within steep channel networks and identify observational targets critical for constraining a debris flow incision law.

Earth Surface Dynamics↗
USGS2014

Resolving terrestrial ecosystem processes along a subgrid topographic gradient for an earth-system model

Soil moisture is a crucial control on surface water and energy fluxes, vegetation, and soil carbon cycling. Earth-system models (ESMs) generally represent an areal-average soil-moisture state in gridcells at scales of 50–200 km and as a result are not able to capture the nonlinear effects of topographically-controlled subgrid heterogeneity in soil moisture, in particular where wetlands are present. We addressed this deficiency by building a subgrid representation of hillslope-scale topographic gradients, TiHy (Tiled-hillslope Hydrology), into the Geophysical Fluid Dynamics Laboratory (GFDL) land model (LM3). LM3-TiHy models one or more representative hillslope geometries for each gridcell by discretizing them into land model tiles hydrologically coupled along an upland-to-lowland gradient. Each tile has its own surface fluxes, vegetation, and vertically-resolved state variables for soil physics and biogeochemistry. LM3-TiHy simulates a gradient in soil moisture and water-table depth between uplands and lowlands in each gridcell. Three hillslope hydrological regimes appear in non-permafrost regions in the model: wet and poorly-drained, wet and well-drained, and dry; with large, small, and zero wetland area predicted, respectively. Compared to the untiled LM3 in stand-alone experiments, LM3-TiHy simulates similar surface energy and water fluxes in the gridcell-mean. However, in marginally wet regions around the globe, LM3-TiHy simulates shallow groundwater in lowlands, leading to higher evapotranspiration, lower surface temperature, and higher leaf area compared to uplands in the same gridcells. Moreover, more than four-fold larger soil carbon concentrations are simulated globally in lowlands as compared with uplands. We compared water-table depths to those simulated by a recent global model-observational synthesis, and we compared wetland and inundated areas diagnosed from the model to observational datasets. The comparisons demonstrate that LM3-TiHy has the capability to represent some of the controls of these hydrological variables, but also that improvement in parameterization and input datasets are needed for more realistic simulations. We found large sensitivity in model-diagnosed wetland and inundated area to the depth of conductive soil and the parameterization of macroporosity. With improved parameterization and inclusion of peatland biogeochemical processes, the model could provide a new approach to investigating the vulnerability of Boreal peatland carbon to climate change in ESMs.

Hydrology and Earth System Sciences↗
USGS1983

Autotrophic processes in meromictic Big Soda Lake, Nevada.

Daily rates of oxygenic photosynthesis (OP) by phytoplankton, anoxygenic photosynthesis (AP) by purple sulfur bacteria, and chemoautotrophic productivity (CP = dark CO2 assimilation) were measured once each season. Total daily productivity and the relative importance of each autotrophic process varied with seasonal changes in vertical mixing, light availability, and the biomass of phototrophs. Daily productivity was highest (2830 mg C.m-2) and was dominated by OP in winter when the mixolimnion was isothermal, the biomass of phytoplankton was high, and the biomass of purple sulfur bacteria was low. During the summer-fall period of thermal stratification, phytoplankton biomass decreased, a plate of purple sulfur bacteria formed below the oxycline, and daily rates of dark CO2 assimilation (CP = 390-680 mg C.m-2) exceeded phototrophic productivity (OP + AP = 200-370 mg C.m-2). Total annual productivity was approx 500 g C.m-2, of which 60% was produced by phytoplankton (mostly in winter), 30% by chemoautotrophs (nitrifying and sulfur-oxidizing bacteria), and only 10% by photosynthetic bacteria. -Authors

Limnology and Oceanography↗